This page is dedicated to talk about my time in the UsefulChem project and what I have learned thus far.

Introduction

• My name is James Giammarco and I am now a junior at Drexel University in my fourth year. I had taken Organic Chemistry I & II with Dr Bradley and discussed with him about working on some research in the future. I went out on my first co-op to Abbey Color and got some industrial experience. I felt that I should seek some research experience when I returned to school. In January of 2006 I took 3 credits worth of research with Dr Bradley who had begun the UsefulChem project. On board at the time was Alicia, & Brett along with a few other undergrads that left a short time after. Other main players eventually came in such as Khalid, and Dave Strumfels. Others came and went but the project grew to a massive online sphere of detail that focused on the synthesis of one specific aldehyde and a range of diketopiperazines that are thought to be anti-malarials.

The Beginning

• The main aspect of this research project is the fact that it is an Opensource project. When I started, Dr. Bradley had already established the UsefulChem blog and listed several avenues of research to pursue. The collaboration of Lawrence W. Bergman a Professor of Microbiology and Immunology at Drexel University College of Medicine along with the library of diketopiperazines from Find-A-Drug that focusing on anti-malarials became a priority. The enzyme that the library of diketopiperazines was thought to inhibit is Enoyl Reductase. The chemistry of the project to synthesize the diketopiperazine initially started with a solid support synthesis to make the diketopiperazines but eventually changed to the one pot Ugi Synthesis. The first task of any research is planning and figuring out our options. "What will we need to do the Ugi synthesis" and "What is available for us to use" were questions to answer. Much of our time in the beginning worked around finding commercially available components that we could use for the Ugi reaction and that fit our diketopiperazine library. As time went on, we came across a few chemical crossroads. One, according to the Ugi synthesis there is one particular aldehyde that is a substituent of the majority of the diketopiperazine library - DOPAL, which is not commercially available. Here is where we had to make a decision, to try and make DOPAL or to substitute it for a similar aldehyde such as phenylacetaldehyde. Substitution was given the go ahead for "mock" Ugi experiments that would in theory make diketopiperazines that should not bind to the Enoyl Reductase sites.

The DOPAL

• During my co-op I worked between making alumina membranes and working on the DOPAL synthesis. It was here that I was able to expand some of my skills and attempt to make DOPAL work. It was not until we found the Robbins(1965) paper that real progress was made. Before that however, I began to see that techniques which seem simple require the most diligence. Even refluxing, the act of keeping a liquid at its boiling point by condensing the liquid vapors, became a technique to master. In previous labs, refluxing seemed simple, just keep the drip going and don't let the vapor rise past a quarter of the condenser length. In all of my trials with DOPAL, having the right amount of Nitrogen gas flowing through the reflux condenser was always a challenge (especially if you don't have a very good valve on the gas cylinder). Refluxing was not the only thing I had to work at, TLCs and eventually NMRs are also on my list of accomplishments during my time on the UsefulChem project.
• For the NMR, I first had to get the minimal training to even handle the instrument alone. Taking simple proton and carbon spectrum don't have much to them...put the sample in, choose the solvent, the number of scans, and go. Taking GOOD NMR requires more prep and more variables to consider. First, you have to understand what your sample is, and for us we are working with solutions that can run at room temperature and have no solids in them. Second, you have to understand what your NMR can do, while Drexel's can't do everything, it has the capabilities for every kind of proton and carbon NMR that we could want such as Correlation Spectroscopy, Distortionless Enhancement by Polarization Transfer, etc. Third, you should know which NMR is best for your needs. The UsefulChem Project has come along way and thus far proton or carbon NMR has been sufficient to answer questions of each experiment. Some of my more interesting work using the NMR has been to transfer our spectra into JCAMP format.
• You might think that yeah I can see how taking an NMR might be challenging...and it is, and I am still learning...but how can a TLC give you trouble? Well if you don't have a decent capillary tube to spot your sample, you have a problem. There are many different ways to solve this; ours became the classic - stretching pipettes. I know that stretching pipettes may not be fun for some, but it works...as long as you don't tough the tip for about a minute after heating it. After a few trials I finally got the knack of a perfect reflux, made better TLCs and began to take better NMRs, however just because you do the technique correctly and well does not mean success with the chemistry. Yes, chemistry is an art. I received the December 4, 2006 issue of C&ENews in the mail and while I can't seem to link to it, there is a very good article on reproducibility by William G Schulz. Here, Schulz has a good quote from a chemistry Professor from Harvard, George M. Whitesides, who says "Sometimes part of the art of chemistry doesn't get included in published papers". I will admit that the first paper we used to make DOPAL we did not follow to the "T" for safety reasons as perchloric acid was a component used at high temperatures, however, it can be frustrating to attempt something again and again and have it seem like no visible improvement has been made. This is in fact not the case. For every 100 experiments done, there are 100 small things learned and they are 100 experiments closer to that 1 in a 1000 that works. Luckily, it did not take 1000 trials to get DOPAL, and in Exp016, success was had! This also brings back into context the Open source nature of the project. All of the "failed" experiments would never be reported in a published paper. Thus everything that we did is available and we try to make it as easily understandable as possible. For the non-scientific folks out there, no matter how descriptive we are, it may not be enough to get the message across. Thus, a collaboration was made with Beth Ritter-Guth who recently posted a nice presentation on the work she has been doing.

The Ugi Synthesis

• Once we had determined that we could successfully make DOPAL, it was on to the big task - make an anti-malarial! Up 'til then, when I thought of chemical reactions, I thought step-wise reactions involving heating, extracting, reheating with additional material, cooling, filtering, etc. Indeed, that is what most of my organic labs had been like. This reaction really boggles my mind. Four components mixed together in a solvent at room temperature to produce a diketopiperazine. Astonishing! Unfortunately, the main paper we were using did not have any kinetics information, nor any fantastic analytical data. This was mine and the group's next challenge. "Will it take an hour or 4 hours or a day or two days or a week", "How much time was actually needed for the reaction" and "Is it better to split it into parts (make it step-wise) rather than keeping it a one pot synthesis" were questions that we were asking ourselves. How does one monitor a reaction and measure the kinetics? Well, you can't just look at the flask and make guesses. The best way to do this was by NMR. Thus far, it is becoming clear that we need to break the reaction apart and really see what turns the crank on this reaction to produce the diketopiperazine. In our Imine page you can see which imines we have made and gotten rate constants for and in our Ugi page, you can see what has been going on with the full reaction. Bearing in mind that we are unsure of the exact mechanism of this reaction, we still have not seen clean results in our NMRs that suggests anything close to our expected Ugi product being made. Experiments to see how each component reacts with the others is being done to see where the side reactions come into play.

Imine Reversal

• For the last few months, in addition to trying to get my own Ugi product, I have been working on the imine reaction. As you can tell from some of our Ugi reactions and especially my experiments:048, 051, 058, 066, 069 after the acid is added to the imine solution, the imine reverts back to the aldehyde. This has given me a really good problem to work on. The most probable reason for the reversal is that the reaction produces too much water. After doing several reactions, it seems obvious to me that if it is water that reverses the reaction, the methanol I am using as a solvent is most likely too wet. I need to do one more reaction with dry methanol to prove this theory. If by chance this does not work, then I will need to look at other amine aldehyde combinations and see if there is any pattern to imine reversal with dry methanol.

Other Experiences

• It was with the UsefulChem project that I got to do have the experience of doing a poster on the research which I helped work on for the Drexel university Research poster day. I also submitted my own version to the NERM in November of 2006. While I did not get to take in too many talks that day, as it was a day trip, I did get to hear a talk by the (at the time) President Elect Katie Hunt. It was an opportunity that I did not want to pass up and as Dr Hunt says "You don't ask, you don't get" so my friends and I asked and about three and half months later got her to talk at Drexel for the ACS student chapter!